SMTL ID : 7b1n.1

Crystal structure of phosphatidyl serine synthase (PSS) in the closed conformation with bound citrate.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x 58A: 5'-O-[(R)-{[(S)-{(2R)-2,3-bis[(9E)-octadec-9-enoyloxy]propoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine(Covalent)

58A.1: 30 residues within 4Å: Chain A: S.33, D.34, T.37, D.63, S.64, D.66, G.67, Y.68, A.70, R.71, T.75, V.76, S.77, G.80, A.81, D.84, F.135, P.139, P.141, A.142, P.178, Y.180, P.181, F.185, I.186, F.189, L.207, Y.211, Y.214 Ligands: CA.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:D.84, A:P.139, A:P.178, A:P.178, A:F.185, A:F.185, A:F.189, A:F.189, A:L.207, A:Y.211, A:Y.211, A:Y.211, A:Y.214 Hydrogen bonds: A:D.34, A:D.34, A:T.37, A:D.66, A:G.67, A:Y.68, A:S.77 Water bridges: A:A.81 Salt bridges: A:R.71 58A.5: 29 residues within 4Å: Chain B: S.33, D.34, T.37, D.63, S.64, D.66, G.67, A.70, R.71, T.75, V.76, S.77, G.80, A.81, D.84, F.135, P.139, P.141, A.142, K.179, Y.180, F.185, I.186, I.188, F.189, L.207, Y.211, Y.214 Ligands: CA.6 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:D.84, B:F.185, B:F.185, B:F.185, B:I.186, B:I.188, B:F.189, B:F.189, B:L.207, B:L.207, B:Y.211, B:Y.214 Hydrogen bonds: B:S.33, B:D.34, B:T.37, B:T.37, B:G.67, B:R.71, B:R.71, B:S.77, B:D.84, B:D.84, B:A.142 Salt bridges: B:K.179, B:K.179

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.63, D.66, D.84 Ligands: 58A.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.63, A:D.63, A:D.66, A:D.84, A:D.84 CA.6: 4 residues within 4Å: Chain B: D.63, D.66, D.84 Ligands: 58A.5 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.63, B:D.63, B:D.66, B:D.84, B:D.84

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: R.123, I.140 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: R.123, F.127, F.135, I.136 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain B: R.123, P.139, I.140, P.141 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: R.123, F.127, I.136 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Centola, M. et al., Crystal structures of phosphatidyl serine synthase PSS reveal the catalytic mechanism of CDP-DAG alcohol O-phosphatidyl transferases. Nat Commun (2021)

Release Date

2021-12-08

Peptides

CDP-diacylglycerol--serine O-phosphatidyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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CDP-diacylglycerol--serine O-phosphatidyltransferase

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